Update notebooks and add examples

fraunhoferportugal · Oct 27, 2021 · aa2ca93 · aa2ca93
1 parent 9f3a332
commit aa2ca93
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Showing 9 changed files with 53 additions and 101 deletions.
diff --git a/notebooks/Query search - 1D.ipynb b/notebooks/Query search - 1D.ipynb
@@ -25,18 +25,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "tq, query = np.loadtxt(\"query_ecg_2.txt\")\n",
-    "ts, sequence = np.loadtxt(\"sequence_ecg_2.txt\")"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 3,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# sequence = sequence[:-500]\n",
-    "# ts = ts[:-500]"
+    "dict_ecg = tssearch.load_ecg_example()\n",
+    "\n",
+    "tq, query = dict_ecg['tq'], dict_ecg['query']\n",
+    "ts, sequence = dict_ecg['ts'], dict_ecg['sequence']"
    ]
   },
   {
@@ -48,7 +40,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [
     {
@@ -84,7 +76,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [
     {
@@ -96,7 +88,7 @@
        "   'parameters': ''}}}"
       ]
      },
-     "execution_count": 5,
+     "execution_count": 4,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -135,7 +127,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 5,
    "metadata": {
     "scrolled": false
    },
@@ -180,36 +172,17 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "from scipy.signal import find_peaks\n",
-    "\n",
-    "# sequence - change T wave\n",
-    "pks = find_peaks(sequence, height=25)\n",
-    "sequence_copy = sequence.copy()\n",
-    "for pk in pks[0][1:-1:2]:\n",
-    "    miu = np.random.choice(np.arange(0,20))\n",
-    "    sequence_copy[pk-5:pk+5] = np.random.normal(miu, 7, 10)\n",
-    "\n",
-    "# query weight\n",
-    "weight = 1 - np.exp(-((np.arange(len(query)) - 40) / 5) ** 2)\n",
-    "weight[weight < 0.1] = 0.1"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [],
    "source": [
-    "\n"
+    "sequence_copy = dict_ecg['sequence_noise'] \n",
+    "weight = dict_ecg['weight']"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [
     {
@@ -240,7 +213,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [
     {
@@ -252,7 +225,7 @@
        "        <AxesSubplot:xlabel='Distance'>], dtype=object)]"
       ]
      },
-     "execution_count": 9,
+     "execution_count": 8,
      "metadata": {},
      "output_type": "execute_result"
     },
@@ -289,7 +262,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [
     {
@@ -346,7 +319,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 10,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -357,7 +330,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 11,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -366,7 +339,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 22,
+   "execution_count": 12,
    "metadata": {},
    "outputs": [
     {

diff --git a/notebooks/Query search - Steps.ipynb b/notebooks/Query search - Steps.ipynb
diff --git a/notebooks/Segmentation.ipynb b/notebooks/Segmentation.ipynb
@@ -25,8 +25,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "tq, query = np.loadtxt(\"query_ecg_2.txt\")\n",
-    "ts, sequence = np.loadtxt(\"sequence_ecg_2.txt\")"
+    "dict_ecg = tssearch.load_ecg_example()\n",
+    "\n",
+    "tq, query = dict_ecg['tq'], dict_ecg['query']\n",
+    "ts, sequence = dict_ecg['ts'], dict_ecg['sequence']"
    ]
   },
   {
@@ -100,7 +102,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [
     {

diff --git a/notebooks/query_ecg_2.txt b/notebooks/query_ecg_2.txt
diff --git a/notebooks/sequence_ecg_2.txt b/notebooks/sequence_ecg_2.txt
diff --git a/tssearch/__init__.py b/tssearch/__init__.py
@@ -1,3 +1,4 @@
 from tssearch.utils import *
 from tssearch.search import *
 from tssearch.distances import *
+from tssearch.examples import *
diff --git a/tssearch/examples/__init__.py b/tssearch/examples/__init__.py
@@ -0,0 +1 @@
+from tssearch.examples.ecg_example_data import *
diff --git a/tssearch/examples/ecg.pickle b/tssearch/examples/ecg.pickle
diff --git a/tssearch/examples/ecg_example_data.py b/tssearch/examples/ecg_example_data.py
@@ -0,0 +1,12 @@
+import tssearch
+import pickle
+import numpy as np
+
+
+def load_ecg_example():
+
+    filename = tssearch.__path__[0] + '/examples/ecg.pickle'
+    with open(filename, 'rb') as handle:
+        data = pickle.load(handle)
+
+    return data
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		from tssearch.examples.ecg_example_data import *